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MMP-potency-prediction

Potency prediction for Matched Molecular Pairs

Repository for the paper: Anatomy of Potency Predictions Focusing on Structural Analogues with Increasing Potency Differences Including Activity Cliffs

Environment

Anaconda can be used to install the .yml file provided.

Notebooks

  • regression_models_mmps.ipynb - generates regression models with a 50/50% random and stratified splits for MMP datasets. (Run before SHAP notebook)
  • regression_models_shap_mmps.ipynb - generates SV/SHAP values for SVR and RFR for MMP test sets.
  • data_final_analysis.ipynb - derives analysis for the computed results, Fig 2, 3 and 4.
  • shap_bit_analysis.ipynb - derives SV/SHAP analysis, Fig 5.
  • shap_mapping.ipynb - Map SV/SHAP values to test compounds.

Folders

  • ML - contains Python scripts to support model building and data analysis.
  • dataset - contains the dataset used in the analysis.
  • ccrlib_master - constains scripts to generate MMP datasets.